vcfR documentation

by
Brian J. Knaus and Niklaus J. Grünwald

GBS class

This material is intended for a one hour class on managing variant call format (VCF) data generated by the genotyping-by-sequencing (GBS) method. This class was a part of GBS_Winter_2017 at Oregon State University. It is assumed that the audience understands the GBS method (i.e., how the data were generated) and has a familiarity with the R language.

Outline

• VCF data
• Extracting data matrices from VCF data
• Plotting depth (or other parameters)
• Quantifying data missingness
• Censoring data outside an acceptance threshold
• Omitting data outside an acceptance threshold
• R’s apply function

The dataset we will be using consists of samples of Phytophthora rubi, P. syringae and P. plurivora that are all mapped to a P. rubi reference. We’ll see that the other species do not map well to the P. rubi genome. This will provide a good example for troubleshooting batch effects in datasets.

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Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.

USDA Agricultural Research Service, Horticultural Crops Research Lab.